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Patterson and molecular replacement techniques, and the use of noncrystallographic symmetry in phasing
International Tables for Crystallography (2010). Vol. B, ch. 2.3, pp. 244-281 [ doi:10.1107/97809553602060000765 ]
... of the structure. 2.3.1.3. Modifications: origin removal, sharpening etc. | | A. L. Patterson, in his first in-depth exposition of his newly ... possible unless a recognizable fragment of known chirality emerges (e.g. L-amino acids in proteins, D-riboses in nucleic acids, the ... asymmetric units within the crystal unit cell. Then there are L symmetry-related heavy-atom sites where . Let the ...
Translation functions
International Tables for Crystallography (2012). Vol. F, ch. 13.3, pp. 347-351 [ doi:10.1107/97809553602060000841 ]
... the observed and the calculated Patterson maps (Crowther & Blow, 1967; Tong, 1993; Navaza & Vernoslova, 1995). Rotation functions are based on ... and the calculated ( Patterson maps throughout the entire unit cell (Tong, 1993), The calculated structure factor is a function of the ... Colman et al., 1976; Read & Schierbeek, 1988; Bentley & Houdusse, 1992; Tong, 1993; Zhang & Matthews, 1994). It is essentially based ...
The locked translation function
International Tables for Crystallography (2012). Vol. F, Section 13.3.8, p. 350 [ doi:10.1107/97809553602060000841 ]
... orientation of the NCS elements in the crystal unit cell (Tong & Rossmann, 1990). Often, an atomic model for the monomer ... all the molecules within the assembly at the same time (Tong & Rossmann, 1997). With the knowledge of the orientations, several ... all the monomers of the assembly at the same time (Tong, 1996b). It can determine the position of the ...
Combined molecular replacement
International Tables for Crystallography (2012). Vol. F, Section 13.3.7, pp. 349-350 [ doi:10.1107/97809553602060000841 ]
... limited six-dimensional search can certainly be performed (Navaza, 1994; Tong, 1996a; Sheriff et al., 1999; Jogl et al., 2001). ... solution (Fujinaga & Read, 1987). The combined-molecular-replacement protocol (Tong, 1996a; Jogl et al., 2001) therefore consists of examining all ... has proven more powerful than conventional methods in structure determinations (Tong, 1996a; Wu et al., 1997). An alternative approach, ...
The unique region of a translation function (the Cheshire group)
International Tables for Crystallography (2012). Vol. F, Section 13.3.6, p. 349 [ doi:10.1107/97809553602060000841 ]
... cell, unless the crystal lattice is centred. References Hirshfeld, F. L. (1968). Symmetry in the generation of trial structures. Acta ...
Packing check in translation functions
International Tables for Crystallography (2012). Vol. F, Section 13.3.5, p. 349 [ doi:10.1107/97809553602060000841 ]
... analysis can be based on the checking of atomic contacts (Tong, 1993). For example, the number of contacts below a ... allowable locations of crystallized macromolecules. Acta Cryst. A32, 778-780. Tong, L. (1993). Replace, a suite of computer programs for ...
Phased translation function
International Tables for Crystallography (2012). Vol. F, Section 13.3.4, p. 349 [ doi:10.1107/97809553602060000841 ]
... Colman et al., 1976; Read & Schierbeek, 1988; Bentley & Houdusse, 1992; Tong, 1993; Zhang & Matthews, 1994). It is essentially based on ... A phased translation function. J. Appl. Cryst. 21, 490-495. Tong, L. (1993). Replace, a suite of computer programs for ...
Patterson-correlation translation function
International Tables for Crystallography (2012). Vol. F, Section 13.3.3, p. 348 [ doi:10.1107/97809553602060000841 ]
... the observed and the calculated Patterson maps (Crowther & Blow, 1967; Tong, 1993; Navaza & Vernoslova, 1995). Rotation functions are based on ... and the calculated ( Patterson maps throughout the entire unit cell (Tong, 1993), The calculated structure factor is a function of the ... of various rotation function programs. Acta Cryst. 21, 872-876. Tong, L. (1993). Replace, a suite of computer programs ...
R-factor and correlation-coefficient translation functions
International Tables for Crystallography (2012). Vol. F, Section 13.3.2, pp. 347-348 [ doi:10.1107/97809553602060000841 ]
R-factor and correlation-coefficient translation functions 13.3.2. R-factor and correlation-coefficient translation functions The crystallographic R factor is often used as an indicator in translation searches. It is a measure of the percentage difference between the observed () and the calculated () structure-factor amplitudes, A similar R factor can be ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 13.3.1, p. 347 [ doi:10.1107/97809553602060000841 ]
... Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). Phaser crystallographic software. J. ... 658-674. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. (2005). Likelihood-enhanced fast translation ...
International Tables for Crystallography (2010). Vol. B, ch. 2.3, pp. 244-281 [ doi:10.1107/97809553602060000765 ]
... of the structure. 2.3.1.3. Modifications: origin removal, sharpening etc. | | A. L. Patterson, in his first in-depth exposition of his newly ... possible unless a recognizable fragment of known chirality emerges (e.g. L-amino acids in proteins, D-riboses in nucleic acids, the ... asymmetric units within the crystal unit cell. Then there are L symmetry-related heavy-atom sites where . Let the ...
Translation functions
International Tables for Crystallography (2012). Vol. F, ch. 13.3, pp. 347-351 [ doi:10.1107/97809553602060000841 ]
... the observed and the calculated Patterson maps (Crowther & Blow, 1967; Tong, 1993; Navaza & Vernoslova, 1995). Rotation functions are based on ... and the calculated ( Patterson maps throughout the entire unit cell (Tong, 1993), The calculated structure factor is a function of the ... Colman et al., 1976; Read & Schierbeek, 1988; Bentley & Houdusse, 1992; Tong, 1993; Zhang & Matthews, 1994). It is essentially based ...
The locked translation function
International Tables for Crystallography (2012). Vol. F, Section 13.3.8, p. 350 [ doi:10.1107/97809553602060000841 ]
... orientation of the NCS elements in the crystal unit cell (Tong & Rossmann, 1990). Often, an atomic model for the monomer ... all the molecules within the assembly at the same time (Tong & Rossmann, 1997). With the knowledge of the orientations, several ... all the monomers of the assembly at the same time (Tong, 1996b). It can determine the position of the ...
Combined molecular replacement
International Tables for Crystallography (2012). Vol. F, Section 13.3.7, pp. 349-350 [ doi:10.1107/97809553602060000841 ]
... limited six-dimensional search can certainly be performed (Navaza, 1994; Tong, 1996a; Sheriff et al., 1999; Jogl et al., 2001). ... solution (Fujinaga & Read, 1987). The combined-molecular-replacement protocol (Tong, 1996a; Jogl et al., 2001) therefore consists of examining all ... has proven more powerful than conventional methods in structure determinations (Tong, 1996a; Wu et al., 1997). An alternative approach, ...
The unique region of a translation function (the Cheshire group)
International Tables for Crystallography (2012). Vol. F, Section 13.3.6, p. 349 [ doi:10.1107/97809553602060000841 ]
... cell, unless the crystal lattice is centred. References Hirshfeld, F. L. (1968). Symmetry in the generation of trial structures. Acta ...
Packing check in translation functions
International Tables for Crystallography (2012). Vol. F, Section 13.3.5, p. 349 [ doi:10.1107/97809553602060000841 ]
... analysis can be based on the checking of atomic contacts (Tong, 1993). For example, the number of contacts below a ... allowable locations of crystallized macromolecules. Acta Cryst. A32, 778-780. Tong, L. (1993). Replace, a suite of computer programs for ...
Phased translation function
International Tables for Crystallography (2012). Vol. F, Section 13.3.4, p. 349 [ doi:10.1107/97809553602060000841 ]
... Colman et al., 1976; Read & Schierbeek, 1988; Bentley & Houdusse, 1992; Tong, 1993; Zhang & Matthews, 1994). It is essentially based on ... A phased translation function. J. Appl. Cryst. 21, 490-495. Tong, L. (1993). Replace, a suite of computer programs for ...
Patterson-correlation translation function
International Tables for Crystallography (2012). Vol. F, Section 13.3.3, p. 348 [ doi:10.1107/97809553602060000841 ]
... the observed and the calculated Patterson maps (Crowther & Blow, 1967; Tong, 1993; Navaza & Vernoslova, 1995). Rotation functions are based on ... and the calculated ( Patterson maps throughout the entire unit cell (Tong, 1993), The calculated structure factor is a function of the ... of various rotation function programs. Acta Cryst. 21, 872-876. Tong, L. (1993). Replace, a suite of computer programs ...
R-factor and correlation-coefficient translation functions
International Tables for Crystallography (2012). Vol. F, Section 13.3.2, pp. 347-348 [ doi:10.1107/97809553602060000841 ]
R-factor and correlation-coefficient translation functions 13.3.2. R-factor and correlation-coefficient translation functions The crystallographic R factor is often used as an indicator in translation searches. It is a measure of the percentage difference between the observed () and the calculated () structure-factor amplitudes, A similar R factor can be ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 13.3.1, p. 347 [ doi:10.1107/97809553602060000841 ]
... Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). Phaser crystallographic software. J. ... 658-674. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. (2005). Likelihood-enhanced fast translation ...
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